Project Details
Projekt
Improving prediction and detection of small proteins for functional analysis in a consortium resembling the functions of the human microbiome
Subject Area
Bioinformatics and Theoretical Biology
Metabolism, Biochemistry and Genetics of Microorganisms
Metabolism, Biochemistry and Genetics of Microorganisms
Term
from 2017 to 2023
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 379643916
Despite the progress in genomics and proteomics over the last decades there is still a blind spot regarding the genomic and proteomic detection of small proteins (sproteins). As a consequence little is known about their functions in prokaryota. From the already known examples it becomes clear that sproteins fulfill a wide variety of functions, some of which are suspected to play a role also in shaping microbial communities. This, however, is the natural form of microbial life and very little is known abouth the role of sProteins in interaction and competition of different species. In this proposal we will investigate a model community resembling the relevant functionalities of the colon microbiota. Among the eight species in this community we will focus on E.coli and L. plantarum.In order to improve the genomic identification of sproteins for E.coli and L. plantarum we propose the improve to RNAcode, a method to identify peptide sequences that are under purifying selection, to reach sufficient sensitivity and specificity for a comprehensive annotation of sproteins in bacterial genomes. This will be achieved by employing a more elaborate statistical model, the replacement of simulations with explicit computations of probabilities, a better handling of alignment errors. Furthermore we will systematically handle the case that the functional peptide is conserved only is a subset of the input sequences. The method will be made available as an integrated data analysis pipeline. As a prerequisite for the mass spectrometry based detection the abundant sproteins have to be enriched by specific protocols. Here we propose the applications of microbeads that exhibit a size exclusion functionality at the shell and different chromatographic features in the core of the beads. The sproteins will be detected either by global as well as targeted proteomics. Subsequently the functions of a selected set of sproteins will be analyzed in terms of sequence features and secondary structure. The secondary structure will be determined from synthesized peptides by Circular Dichroism and Fourier infrared spectroscopy. In addition potential interaction partners will be identified after biotin-tagging and affinity purification. The close interaction between the bioinformatic and proteomic approach will allow us to improve the aspects of prediction, enrichment, detection and functional validation of small proteins in bacteria. Hence we are aiming at identifying novel sproteins and the mechanisms how they shape microbial communities.
DFG Programme
Priority Programmes
